Contacts of the helix formed by residues 210 - 224 (chain A) in PDB entry 6TOS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ASP* 2.9 10.3 + - - +
209A ASP* 1.3 76.1 - - - +
211A ALA* 1.4 66.1 + - - +
213A LYS* 3.0 17.5 + - + +
214A ILE* 3.1 39.7 + - + +
407A SOG 3.9 46.1 - - + -
418A SOG 4.2 41.1 - - + -
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Residues in contact with ALA 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TRP* 3.8 21.0 - - + -
208A ASP* 3.1 23.6 + - - +
210A LEU* 1.4 74.5 - - - +
212A PRO* 1.4 64.2 - - + +
213A LYS 3.2 0.5 + - - -
214A ILE* 3.2 7.7 + - - +
215A TYR* 3.0 28.8 + - - +
408A SOG 4.6 14.4 - - + +
404B PGW 4.2 12.4 - - + +
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Residues in contact with PRO 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TRP* 3.6 39.0 - - + +
208A ASP 3.1 26.2 - - - +
209A ASP 3.8 0.4 - - - +
210A LEU 3.7 2.2 - - - -
211A ALA* 1.4 83.2 - - + +
213A LYS* 1.3 55.1 + - - +
216A HIS* 2.9 40.6 + - + +
322A ARG 4.1 2.6 - - - +
403A CIT 3.3 51.6 - - + +
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Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASP* 3.4 17.0 - - - +
210A LEU* 3.0 8.0 + - - +
212A PRO* 1.3 74.3 - - - +
214A ILE* 1.3 62.8 + - - +
217A SER* 2.7 33.8 + - - -
322A ARG 3.5 16.8 - - - +
323A VAL* 3.7 9.8 + - - +
403A CIT 3.7 20.4 + - - +
407A SOG 3.1 64.0 + - + +
412A SOG 2.8 41.1 + - - +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 3.1 44.7 + - + +
211A ALA* 3.9 7.9 - - - +
213A LYS* 1.3 75.4 - - - +
215A TYR* 1.3 58.7 + - - +
217A SER* 3.7 1.6 - - - -
218A CYS* 3.0 34.2 + - - -
407A SOG 4.2 20.4 - - + -
225B LEU* 3.7 31.4 - - + -
404B PGW 4.0 23.8 - - + -
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE 5.2 0.9 + - - -
176A MET* 4.7 4.3 - - - -
178A PRO* 4.2 17.3 - - + -
179A GLN* 2.7 46.3 + - - +
182A VAL* 5.6 0.7 - - + -
206A TRP* 3.6 33.4 - + + -
211A ALA 3.0 17.0 + - - +
212A PRO 4.1 1.3 - - - +
214A ILE* 1.3 77.6 - - - +
216A HIS* 1.3 76.6 + + - +
218A CYS* 3.4 3.8 + - - +
219A PHE* 2.8 48.7 + + + +
404B PGW 3.8 55.1 - - + +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLU* 2.7 41.1 + - - -
212A PRO* 2.9 36.1 + - + +
215A TYR* 1.3 86.3 - + - +
217A SER* 1.3 64.9 + - - +
219A PHE* 3.8 6.0 - - - +
220A PHE* 3.1 23.9 + - - +
318A ASN* 4.6 17.2 - - + +
319A VAL* 4.2 3.8 - - - +
322A ARG* 3.4 40.3 - - + +
323A VAL* 4.1 9.0 - - + -
401A NRE 3.5 26.4 - - + +
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Residues in contact with SER 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS 2.7 23.7 + - - -
214A ILE 3.7 4.0 - - - -
216A HIS* 1.3 77.5 - - - +
218A CYS* 1.4 60.8 + - - +
220A PHE* 3.3 6.3 + - - +
221A ILE* 3.1 32.1 + - - +
319A VAL* 5.3 2.1 - - - +
323A VAL* 3.4 17.1 - - - +
407A SOG 3.3 30.5 - - - +
221B ILE* 5.1 3.8 - - - -
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Residues in contact with CYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.0 26.1 + - - +
215A TYR 3.7 4.3 - - - +
217A SER* 1.4 70.4 - - - +
219A PHE* 1.4 60.2 + - - +
221A ILE 3.8 0.2 - - - -
222A VAL* 2.9 36.7 + - - +
407A SOG 5.3 1.1 - - - -
221B ILE* 4.0 26.5 - - + -
225B LEU* 3.9 28.9 - - - -
226B ALA* 4.6 4.7 - - + -
404B PGW 3.8 36.3 - - + -
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Residues in contact with PHE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ALA* 4.4 2.5 - - + -
130A VAL* 4.8 13.7 - - + -
176A MET* 3.6 33.2 - - + -
215A TYR* 2.8 45.4 + + + +
216A HIS* 3.8 11.0 - - - +
217A SER 3.4 0.2 - - - -
218A CYS* 1.4 71.3 - - - +
220A PHE* 1.3 55.7 + - - +
223A THR* 2.7 58.5 + - + +
315A SER* 5.9 2.9 - - - -
318A ASN* 5.9 3.8 - - + -
401A NRE 3.6 48.9 - - + -
404B PGW 4.4 13.6 - - + +
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Residues in contact with PHE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A HIS 3.1 17.7 + - - +
217A SER* 3.6 4.9 - - - +
219A PHE* 1.3 80.5 - - - +
221A ILE* 1.3 67.7 + - + +
223A THR* 4.5 2.5 - - - -
224A TYR* 3.0 54.7 + + + +
225A LEU* 3.0 37.4 + - + -
312A LEU* 5.7 1.3 - - + -
315A SER* 3.7 38.4 - - - +
316A VAL* 4.7 12.8 - - + -
319A VAL* 3.6 21.5 - - + -
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 3.1 18.1 + - - +
220A PHE* 1.3 87.1 - - + +
222A VAL* 1.3 61.9 + - - +
225A LEU* 4.1 12.1 - - + -
226A ALA* 2.9 36.4 + - + +
227A PRO* 3.5 1.0 - - - +
217B SER* 4.5 16.4 - - - +
218B CYS* 3.8 35.2 - - + +
221B ILE* 3.3 48.2 - - + -
222B VAL* 4.2 3.8 - - + -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A VAL* 4.7 2.1 - - - +
135A LEU* 6.1 0.9 - - - +
175A ILE* 5.0 9.0 - - + -
218A CYS 2.9 20.5 + - - +
221A ILE* 1.3 78.1 - - - +
223A THR* 1.4 60.4 + - + +
226A ALA* 5.1 0.2 - - - -
227A PRO* 3.2 20.3 - - - +
221B ILE* 4.0 11.4 - - + -
222B VAL* 4.7 3.1 - - + -
226B ALA* 3.8 28.0 - - + -
230B LEU* 6.3 1.1 - - + -
404B PGW 3.8 53.2 - - + -
405B PGW 4.3 9.7 - - + +
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Residues in contact with THR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL* 4.3 20.2 - - + +
131A SER* 4.9 7.2 - - - -
134A VAL* 3.4 30.3 - - + +
175A ILE* 5.7 0.9 - - + -
176A MET* 3.8 29.8 - - + -
219A PHE* 2.7 51.2 + - + +
220A PHE* 4.4 0.7 + - - -
222A VAL* 1.4 77.4 - - + +
224A TYR* 1.3 64.5 + - - +
227A PRO* 4.2 3.6 - - - -
307A PHE* 4.8 2.9 - - - -
315A SER* 5.7 0.5 + - - -
404B PGW 4.3 8.1 - - + -
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Residues in contact with TYR 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.0 35.3 + + + +
222A VAL 3.6 0.8 - - - -
223A THR* 1.3 85.6 + - - +
225A LEU* 1.3 76.6 + - + +
226A ALA 3.7 1.1 - - - -
227A PRO* 3.6 2.6 - - - +
228A LEU* 3.2 56.8 + - + +
307A PHE* 5.3 1.1 - + - -
308A ALA* 2.7 36.4 + - - +
311A TYR* 3.7 26.7 - + + -
312A LEU* 3.5 28.3 - - + +
315A SER* 3.6 24.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il